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Plant Physiol, May 2003, Vol. 132, pp. 118-136
Clustering of Microarray Data Reveals Transcript Patterns
Associated with Somatic Embryogenesis in
Soybean1,[w]
Françoise
Thibaud-Nissen,
Robin T.
Shealy,
Anupama
Khanna, and
Lila O.
Vodkin*
Department of Crop Sciences, University of Illinois
Urbana-Champaign, Urbana, Illinois 61801
Globular somatic embryos can be induced from immature
cotyledons of soybean (Glycine max L. Merr. cv Jack)
placed on high levels of the auxin 2,4-dichlorophenoxyacetic
acid (2,4-D). Somatic embryos develop from the adaxial side of the
cotyledon, whereas the abaxial side evolves into a callus. Using a
9,280-cDNA clone array, we have compared steady-state RNA from the
adaxial side from which embryos develop and from the abaxial callus at
five time points over the course of the 4 weeks necessary for the
development of globular embryos. In a second set of experiments, we
have profiled the expression of each clone in the adaxial side during
the same period. A total of 495 genes differentially expressed in at
least one of these experiments were grouped according to the similarity of their expression profiles using a nonhierarchical clustering algorithm. Our results indicate that the appearance of somatic embryos
is preceded by dedifferentiation of the cotyledon during the first 2 weeks on auxin. Changes in mRNA abundance of genes characteristic of
oxidative stress and genes indicative of cell division in the adaxial
side of the cotyledons suggest that the arrangement of the new cells
into organized structures might depend on a genetically controlled
balance between cell proliferation and cell death. Our data also
suggest that the formation of somatic globular embryos is accompanied
by the transcription of storage proteins and the synthesis of
gibberellic acid.
1
This work was supported by the National Science
Foundation Plant Genome Research Program as part of a "Functional
Genomics Project for Soybean" (grant no. DBI-9872565) and by grants
from the United Soybean Board.
[w]
The online version of this article contains Web-only
data. The supplemental material is available at
www.plantphysiol.org.
*
Corresponding author; e-mail l-vodkin{at}uiuc.edu; fax
217-333-4582.
© 2003 American Society of Plant Biologists
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